Starting phenix.real_space_refine on Wed Sep 17 13:26:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.map" model { file = "/net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vow_43393/09_2025/8vow_43393.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5776 2.51 5 N 1444 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8917 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4430 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 10, 'TRANS': 555} Chain: "B" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4422 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 10, 'TRANS': 554} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 8917 At special positions: 0 Unit cell: (70.523, 97.05, 140.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 30 16.00 P 5 15.00 Mg 2 11.99 O 1659 8.00 N 1444 7.00 C 5776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 280.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 70.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.539A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.587A pdb=" N LEU A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 251 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.897A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.700A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.842A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 4.668A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 326 Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.736A pdb=" N GLN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.627A pdb=" N LEU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.819A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 436 through 464 Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.542A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.624A pdb=" N GLY A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.703A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.511A pdb=" N LYS A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.580A pdb=" N LEU A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 removed outlier: 3.622A pdb=" N TYR A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 3.542A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.957A pdb=" N GLN A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 721 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 188 removed outlier: 4.005A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 202 through 251 removed outlier: 3.585A pdb=" N ILE B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.763A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.631A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.898A pdb=" N ALA B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.680A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 307 through 354 removed outlier: 4.364A pdb=" N ILE B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 417 Processing helix chain 'B' and resid 421 through 432 removed outlier: 3.515A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 436 through 464 Proline residue: B 447 - end of helix removed outlier: 3.752A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.856A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.855A pdb=" N LEU B 497 " --> pdb=" O ARG B 494 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 498 " --> pdb=" O TYR B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 498' Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.731A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 639 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.501A pdb=" N THR B 683 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.526A pdb=" N PHE A 493 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 491 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 489 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 542 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.759A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP A 647 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 565 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 515 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 693 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 509 removed outlier: 6.254A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 645 through 647 removed outlier: 8.994A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 700 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS B 694 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 573 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2825 1.36 - 1.50: 2155 1.50 - 1.63: 4010 1.63 - 1.77: 0 1.77 - 1.91: 64 Bond restraints: 9054 Sorted by residual: bond pdb=" CA TYR A 691 " pdb=" CB TYR A 691 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.38e-02 5.25e+03 3.74e+00 bond pdb=" C TYR A 691 " pdb=" O TYR A 691 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.19e-02 7.06e+03 1.77e+00 bond pdb=" C ARG A 494 " pdb=" N TYR A 495 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.40e-02 5.10e+03 1.67e+00 bond pdb=" C ASP A 671 " pdb=" N VAL A 672 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.05e-02 9.07e+03 1.63e+00 bond pdb=" CA ASP A 671 " pdb=" C ASP A 671 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.51e-02 4.39e+03 1.53e+00 ... (remaining 9049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11997 1.69 - 3.38: 176 3.38 - 5.07: 34 5.07 - 6.76: 13 6.76 - 8.45: 2 Bond angle restraints: 12222 Sorted by residual: angle pdb=" O ASP A 670 " pdb=" C ASP A 670 " pdb=" N ASP A 671 " ideal model delta sigma weight residual 122.19 124.83 -2.64 1.03e+00 9.43e-01 6.54e+00 angle pdb=" N GLN B 446 " pdb=" CA GLN B 446 " pdb=" C GLN B 446 " ideal model delta sigma weight residual 109.81 115.16 -5.35 2.21e+00 2.05e-01 5.87e+00 angle pdb=" CA LEU B 610 " pdb=" CB LEU B 610 " pdb=" CG LEU B 610 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" C ARG A 680 " pdb=" N LEU A 681 " pdb=" CA LEU A 681 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.13e+00 angle pdb=" O2B ADP B 801 " pdb=" PB ADP B 801 " pdb=" O3B ADP B 801 " ideal model delta sigma weight residual 119.90 113.17 6.73 3.00e+00 1.11e-01 5.04e+00 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4871 17.94 - 35.88: 499 35.88 - 53.81: 89 53.81 - 71.75: 20 71.75 - 89.69: 9 Dihedral angle restraints: 5488 sinusoidal: 2215 harmonic: 3273 Sorted by residual: dihedral pdb=" CA LEU A 497 " pdb=" C LEU A 497 " pdb=" N ARG A 498 " pdb=" CA ARG A 498 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ARG B 269 " pdb=" C ARG B 269 " pdb=" N PHE B 270 " pdb=" CA PHE B 270 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 606 " pdb=" CG GLU A 606 " pdb=" CD GLU A 606 " pdb=" OE1 GLU A 606 " ideal model delta sinusoidal sigma weight residual 0.00 -89.69 89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 969 0.032 - 0.063: 327 0.063 - 0.094: 109 0.094 - 0.126: 47 0.126 - 0.157: 8 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CB ILE B 280 " pdb=" CA ILE B 280 " pdb=" CG1 ILE B 280 " pdb=" CG2 ILE B 280 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE B 509 " pdb=" N ILE B 509 " pdb=" C ILE B 509 " pdb=" CB ILE B 509 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE B 690 " pdb=" N ILE B 690 " pdb=" C ILE B 690 " pdb=" CB ILE B 690 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1457 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 446 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 447 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 684 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ILE B 684 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE B 684 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 685 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 508 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C THR B 508 " 0.020 2.00e-02 2.50e+03 pdb=" O THR B 508 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE B 509 " -0.007 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 53 2.51 - 3.11: 6793 3.11 - 3.71: 13810 3.71 - 4.30: 18731 4.30 - 4.90: 32226 Nonbonded interactions: 71613 Sorted by model distance: nonbonded pdb=" O2B ADP B 801 " pdb="MG MG B 803 " model vdw 1.916 2.170 nonbonded pdb=" O4 VO4 B 802 " pdb="MG MG B 803 " model vdw 1.923 2.170 nonbonded pdb=" O1 VO4 B 802 " pdb="MG MG B 803 " model vdw 1.924 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.999 2.170 nonbonded pdb=" O3B ATP A 801 " pdb="MG MG A 802 " model vdw 2.049 2.170 ... (remaining 71608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 158 through 722 or resid 802)) selection = (chain 'B' and (resid 158 through 722 or resid 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9054 Z= 0.129 Angle : 0.555 8.451 12222 Z= 0.280 Chirality : 0.039 0.157 1460 Planarity : 0.003 0.037 1504 Dihedral : 15.065 89.689 3378 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.21 % Allowed : 0.10 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.26), residues: 1127 helix: 2.36 (0.20), residues: 725 sheet: -0.77 (0.77), residues: 35 loop : -2.19 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.017 0.001 TYR B 495 PHE 0.018 0.001 PHE A 715 TRP 0.003 0.001 TRP B 409 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9054) covalent geometry : angle 0.55466 (12222) hydrogen bonds : bond 0.12358 ( 573) hydrogen bonds : angle 4.46307 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.397 Fit side-chains REVERT: A 680 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7555 (tpt170) REVERT: B 302 TYR cc_start: 0.8084 (t80) cc_final: 0.7785 (t80) REVERT: B 554 SER cc_start: 0.8319 (p) cc_final: 0.8010 (p) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.0789 time to fit residues: 18.5532 Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 627 GLN A 679 HIS ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133343 restraints weight = 11959.479| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.79 r_work: 0.3505 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9054 Z= 0.121 Angle : 0.531 9.202 12222 Z= 0.266 Chirality : 0.039 0.156 1460 Planarity : 0.003 0.036 1504 Dihedral : 7.576 66.069 1238 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.44 % Allowed : 9.66 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.26), residues: 1127 helix: 2.60 (0.20), residues: 732 sheet: -1.01 (0.73), residues: 35 loop : -2.35 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 680 TYR 0.014 0.001 TYR B 495 PHE 0.033 0.001 PHE B 435 TRP 0.008 0.001 TRP A 718 HIS 0.003 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9054) covalent geometry : angle 0.53112 (12222) hydrogen bonds : bond 0.04374 ( 573) hydrogen bonds : angle 3.77324 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.337 Fit side-chains REVERT: A 718 TRP cc_start: 0.8212 (t-100) cc_final: 0.7901 (t-100) REVERT: B 554 SER cc_start: 0.8398 (p) cc_final: 0.8075 (p) REVERT: B 629 GLN cc_start: 0.7580 (mt0) cc_final: 0.7259 (tt0) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.0780 time to fit residues: 16.6298 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 627 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132444 restraints weight = 11954.060| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.80 r_work: 0.3497 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9054 Z= 0.117 Angle : 0.513 8.968 12222 Z= 0.260 Chirality : 0.039 0.141 1460 Planarity : 0.003 0.036 1504 Dihedral : 7.497 65.649 1238 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.13 % Allowed : 11.92 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.26), residues: 1127 helix: 2.66 (0.20), residues: 733 sheet: -1.12 (0.71), residues: 35 loop : -2.32 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.013 0.001 TYR B 225 PHE 0.019 0.001 PHE B 435 TRP 0.005 0.001 TRP A 718 HIS 0.010 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9054) covalent geometry : angle 0.51262 (12222) hydrogen bonds : bond 0.04255 ( 573) hydrogen bonds : angle 3.68070 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.348 Fit side-chains REVERT: A 687 LEU cc_start: 0.6399 (mm) cc_final: 0.6196 (mm) REVERT: A 718 TRP cc_start: 0.8182 (t-100) cc_final: 0.7971 (t-100) REVERT: B 277 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7446 (ttm-80) REVERT: B 353 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7712 (mmtt) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.0841 time to fit residues: 16.9178 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 679 HIS A 720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131112 restraints weight = 12203.856| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.81 r_work: 0.3482 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9054 Z= 0.122 Angle : 0.513 9.129 12222 Z= 0.257 Chirality : 0.039 0.138 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.444 65.103 1238 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.44 % Allowed : 12.95 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1127 helix: 2.66 (0.19), residues: 735 sheet: -1.20 (0.69), residues: 35 loop : -2.31 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.015 0.001 TYR B 495 PHE 0.016 0.001 PHE B 217 TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9054) covalent geometry : angle 0.51326 (12222) hydrogen bonds : bond 0.04277 ( 573) hydrogen bonds : angle 3.62411 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.286 Fit side-chains REVERT: B 353 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7760 (tptt) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 0.0845 time to fit residues: 17.0975 Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 109 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131593 restraints weight = 12081.504| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.81 r_work: 0.3488 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9054 Z= 0.114 Angle : 0.502 9.189 12222 Z= 0.254 Chirality : 0.039 0.139 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.341 64.057 1238 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.44 % Allowed : 15.21 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.26), residues: 1127 helix: 2.67 (0.19), residues: 740 sheet: -1.06 (0.71), residues: 35 loop : -2.36 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.014 0.001 TYR B 495 PHE 0.015 0.001 PHE B 217 TRP 0.003 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9054) covalent geometry : angle 0.50178 (12222) hydrogen bonds : bond 0.04181 ( 573) hydrogen bonds : angle 3.56921 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.226 Fit side-chains REVERT: A 627 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7497 (mm-40) REVERT: A 671 ASP cc_start: 0.8125 (p0) cc_final: 0.7876 (p0) REVERT: B 353 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7755 (tptt) outliers start: 14 outliers final: 11 residues processed: 138 average time/residue: 0.0828 time to fit residues: 16.3760 Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131809 restraints weight = 12146.448| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.84 r_work: 0.3486 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9054 Z= 0.118 Angle : 0.517 9.100 12222 Z= 0.258 Chirality : 0.039 0.156 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.285 63.610 1238 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.75 % Allowed : 15.62 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.26), residues: 1127 helix: 2.69 (0.19), residues: 736 sheet: -1.01 (0.70), residues: 35 loop : -2.34 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.013 0.001 TYR B 495 PHE 0.018 0.001 PHE A 604 TRP 0.003 0.001 TRP A 718 HIS 0.002 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9054) covalent geometry : angle 0.51717 (12222) hydrogen bonds : bond 0.04174 ( 573) hydrogen bonds : angle 3.55321 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.295 Fit side-chains REVERT: A 236 MET cc_start: 0.7447 (ttp) cc_final: 0.7169 (tpp) REVERT: A 495 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 589 MET cc_start: 0.7704 (tpt) cc_final: 0.7267 (tpt) REVERT: A 659 ASN cc_start: 0.7307 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 671 ASP cc_start: 0.8131 (p0) cc_final: 0.7871 (p0) REVERT: A 687 LEU cc_start: 0.6286 (mm) cc_final: 0.5894 (mm) REVERT: B 277 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7449 (ttm-80) REVERT: B 353 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7768 (tptt) REVERT: B 464 GLU cc_start: 0.7877 (tp30) cc_final: 0.7485 (tp30) outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 0.0845 time to fit residues: 16.6081 Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131400 restraints weight = 12144.015| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.84 r_work: 0.3485 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9054 Z= 0.118 Angle : 0.523 9.089 12222 Z= 0.259 Chirality : 0.039 0.194 1460 Planarity : 0.003 0.033 1504 Dihedral : 7.244 63.128 1238 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.64 % Allowed : 16.34 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1127 helix: 2.71 (0.19), residues: 734 sheet: -0.86 (0.71), residues: 35 loop : -2.32 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.013 0.001 TYR B 495 PHE 0.015 0.001 PHE B 217 TRP 0.002 0.001 TRP B 409 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9054) covalent geometry : angle 0.52330 (12222) hydrogen bonds : bond 0.04172 ( 573) hydrogen bonds : angle 3.54481 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.362 Fit side-chains REVERT: A 495 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6866 (t80) REVERT: A 589 MET cc_start: 0.7691 (tpt) cc_final: 0.7224 (tpt) REVERT: A 671 ASP cc_start: 0.8153 (p0) cc_final: 0.7890 (p0) REVERT: B 353 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7745 (tptt) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.0867 time to fit residues: 17.1082 Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.0570 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132772 restraints weight = 12107.508| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.84 r_work: 0.3505 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9054 Z= 0.108 Angle : 0.514 9.672 12222 Z= 0.256 Chirality : 0.038 0.142 1460 Planarity : 0.003 0.032 1504 Dihedral : 7.137 62.156 1238 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.23 % Allowed : 16.75 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.26), residues: 1127 helix: 2.72 (0.19), residues: 735 sheet: -0.77 (0.72), residues: 35 loop : -2.27 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.013 0.001 TYR B 225 PHE 0.017 0.001 PHE A 715 TRP 0.003 0.001 TRP B 409 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9054) covalent geometry : angle 0.51388 (12222) hydrogen bonds : bond 0.04029 ( 573) hydrogen bonds : angle 3.51653 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.376 Fit side-chains REVERT: A 495 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6964 (t80) REVERT: A 589 MET cc_start: 0.7735 (tpt) cc_final: 0.7327 (tpt) REVERT: A 671 ASP cc_start: 0.8097 (p0) cc_final: 0.7846 (p0) REVERT: A 687 LEU cc_start: 0.6334 (mm) cc_final: 0.6019 (mm) REVERT: B 196 ASP cc_start: 0.7564 (m-30) cc_final: 0.7253 (m-30) REVERT: B 353 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7772 (tptt) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.0961 time to fit residues: 18.1139 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130779 restraints weight = 12062.525| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.82 r_work: 0.3477 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9054 Z= 0.128 Angle : 0.531 9.867 12222 Z= 0.264 Chirality : 0.039 0.140 1460 Planarity : 0.003 0.032 1504 Dihedral : 7.197 62.638 1238 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.44 % Allowed : 16.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 1127 helix: 2.62 (0.19), residues: 733 sheet: -0.78 (0.73), residues: 35 loop : -2.33 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 498 TYR 0.018 0.001 TYR B 389 PHE 0.015 0.001 PHE B 217 TRP 0.003 0.001 TRP A 718 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9054) covalent geometry : angle 0.53125 (12222) hydrogen bonds : bond 0.04277 ( 573) hydrogen bonds : angle 3.56845 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.355 Fit side-chains REVERT: A 285 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7533 (tt) REVERT: A 495 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.6999 (t80) REVERT: A 589 MET cc_start: 0.7737 (tpt) cc_final: 0.7307 (tpt) REVERT: A 687 LEU cc_start: 0.6419 (mm) cc_final: 0.6132 (mm) REVERT: B 196 ASP cc_start: 0.7579 (m-30) cc_final: 0.7277 (m-30) REVERT: B 353 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7776 (tptt) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.0908 time to fit residues: 17.1267 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131330 restraints weight = 12063.335| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.82 r_work: 0.3486 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9054 Z= 0.123 Angle : 0.541 10.079 12222 Z= 0.268 Chirality : 0.039 0.140 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.156 62.080 1238 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.34 % Allowed : 16.75 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1127 helix: 2.65 (0.20), residues: 731 sheet: -0.70 (0.75), residues: 35 loop : -2.26 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.012 0.001 TYR B 225 PHE 0.021 0.001 PHE A 715 TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9054) covalent geometry : angle 0.54150 (12222) hydrogen bonds : bond 0.04248 ( 573) hydrogen bonds : angle 3.56703 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.374 Fit side-chains REVERT: A 285 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7487 (tt) REVERT: A 495 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 589 MET cc_start: 0.7694 (tpt) cc_final: 0.7246 (tpt) REVERT: A 687 LEU cc_start: 0.6477 (mm) cc_final: 0.6207 (mm) REVERT: B 353 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7754 (tptt) REVERT: B 700 GLU cc_start: 0.8404 (pm20) cc_final: 0.8106 (pm20) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.0868 time to fit residues: 16.6093 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 0.0060 chunk 8 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.156590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132992 restraints weight = 11894.292| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.80 r_work: 0.3513 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9054 Z= 0.112 Angle : 0.540 10.430 12222 Z= 0.266 Chirality : 0.039 0.143 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.073 61.192 1238 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.23 % Allowed : 17.06 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1127 helix: 2.67 (0.19), residues: 735 sheet: -0.61 (0.76), residues: 35 loop : -2.25 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.013 0.001 TYR B 225 PHE 0.014 0.001 PHE B 217 TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9054) covalent geometry : angle 0.54008 (12222) hydrogen bonds : bond 0.04107 ( 573) hydrogen bonds : angle 3.52573 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.49 seconds wall clock time: 38 minutes 5.58 seconds (2285.58 seconds total)